Base de dados : MEDLINE
Pesquisa : D08.244.453.012 [Categoria DeCS]
Referências encontradas : 429 [refinar]
Mostrando: 1 .. 10   no formato [Detalhado]

página 1 de 43 ir para página                         

  1 / 429 MEDLINE  
              next record last record
seleciona
para imprimir
Fotocópia
Texto completo
[PMID]:28923662
[Au] Autor:Kammoonah S; Prasad B; Balaraman P; Mundhada H; Schwaneberg U; Plettner E
[Ad] Endereço:Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.
[Ti] Título:Selecting of a cytochrome P450 SeSaM library with 3-chloroindole and endosulfan - Identification of mutants that dehalogenate 3-chloroindole.
[So] Source:Biochim Biophys Acta;1866(1):68-79, 2018 01.
[Is] ISSN:0006-3002
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Cytochrome P450 (a camphor hydroxylase) from the soil bacterium Pseudomonas putida shows potential importance in environmental applications such as the degradation of chlorinated organic pollutants. Seven P450 mutants generated from Sequence Saturation Mutagenesis (SeSaM) and isolated by selection on minimal media with either 3-chloroindole or the insecticide endosulfan were studied for their ability to oxidize of 3-chloroindole to isatin. The wild-type enzyme did not accept 3-chloroindole as a substrate. Mutant (E156G/V247F/V253G/F256S) had the highest maximal velocity in the conversion of 3-chloroindole to isatin, whereas mutants (T56A/N116H/D297N) and (G60S/Y75H) had highest k /K values. Six of the mutants had more than one mutation, and within this set, mutation of residues 297 and 179 was observed twice. Docking simulations were performed on models of the mutant enzymes; the wild-type did not accommodate 3-chloroindole in the active site, whereas all the mutants did. We propose two potential reaction pathways for dechlorination of 3-chloroindole. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.
[Mh] Termos MeSH primário: Proteínas de Bactérias/química
Cânfora 5-Mono-Oxigenase/química
Endossulfano/metabolismo
Biblioteca Gênica
Indóis/metabolismo
Pseudomonas putida/enzimologia
[Mh] Termos MeSH secundário: Motivos de Aminoácidos
Substituição de Aminoácidos
Proteínas de Bactérias/genética
Proteínas de Bactérias/metabolismo
Sítios de Ligação
Biodegradação Ambiental
Cânfora 5-Mono-Oxigenase/genética
Cânfora 5-Mono-Oxigenase/metabolismo
Clonagem Molecular
Endossulfano/química
Escherichia coli/genética
Escherichia coli/metabolismo
Expressão Gênica
Halogenação
Indóis/química
Isatina/química
Isatina/metabolismo
Cinética
Simulação de Acoplamento Molecular
Mutação
Oxirredução
Ligação Proteica
Domínios e Motivos de Interação entre Proteínas
Estrutura Secundária de Proteína
Pseudomonas putida/química
Proteínas Recombinantes/química
Proteínas Recombinantes/genética
Proteínas Recombinantes/metabolismo
Especificidade por Substrato
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Bacterial Proteins); 0 (Indoles); 0 (Recombinant Proteins); 82X95S7M06 (Isatin); EC 1.14.15.1 (Camphor 5-Monooxygenase); OKA6A6ZD4K (Endosulfan)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180208
[Lr] Data última revisão:
180208
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170920
[St] Status:MEDLINE


  2 / 429 MEDLINE  
              first record previous record next record last record
seleciona
para imprimir
Fotocópia
Texto completo
[PMID]:28473297
[Au] Autor:Pochapsky TC; Wong N; Zhuang Y; Futcher J; Pandelia ME; Teitz DR; Colthart AM
[Ad] Endereço:Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, USA. Electronic address: pochapsk@brandeis.edu.
[Ti] Título:NADH reduction of nitroaromatics as a probe for residual ferric form high-spin in a cytochrome P450.
[So] Source:Biochim Biophys Acta;1866(1):126-133, 2018 01.
[Is] ISSN:0006-3002
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:The existence of a substrate-sensitive equilibrium between high spin (S=5/2) and low spin (S=1/2) ferric iron is a well-established phenomenon in the cytochrome P450 (CYP) superfamily, although its origins are still a subject of discussion. A series of mutations that strongly perturb the spin state equilibrium in the camphor hydroxylase CYP101A1 were recently described (Colthart et al., Sci. Rep. 6, 22035 (2016)). Wild type CYP101A1 as well as some CYP101A1 mutants are herein shown to be capable of catalyzing the reduction of nitroacetophenones by NADH to the corresponding anilino compounds (nitroreductase or NRase activity). The distinguishing characteristic between those mutants that catalyze the reduction and those that cannot appears to be the extent to which residual high spin form exists in the absence of the native substrate d-camphor, with those showing the largest spin state shifts upon camphor binding also exhibiting NRase activity. Optical and EPR spectroscopy was used to further examine these phenomena. These results suggest that reduction of nitroaromatics may provide a useful probe of residual high spin states in the CYP superfamily. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.
[Mh] Termos MeSH primário: Acetofenonas/química
Proteínas de Bactérias/química
Cânfora 5-Mono-Oxigenase/química
Cânfora/química
Compostos Férricos/química
Heme/química
NAD/química
[Mh] Termos MeSH secundário: Acetofenonas/metabolismo
Motivos de Aminoácidos
Proteínas de Bactérias/genética
Proteínas de Bactérias/metabolismo
Sítios de Ligação
Biocatálise
Cânfora/metabolismo
Cânfora 5-Mono-Oxigenase/genética
Cânfora 5-Mono-Oxigenase/metabolismo
Clonagem Molecular
Espectroscopia de Ressonância de Spin Eletrônica
Escherichia coli/genética
Escherichia coli/metabolismo
Expressão Gênica
Heme/metabolismo
Cinética
Modelos Moleculares
NAD/metabolismo
Oxirredução
Ligação Proteica
Conformação Proteica em alfa-Hélice
Conformação Proteica em Folha beta
Domínios e Motivos de Interação entre Proteínas
Proteínas Recombinantes/química
Proteínas Recombinantes/genética
Proteínas Recombinantes/metabolismo
Especificidade por Substrato
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL
[Nm] Nome de substância:
0 (Acetophenones); 0 (Bacterial Proteins); 0 (Ferric Compounds); 0 (Recombinant Proteins); 0U46U6E8UK (NAD); 100-19-6 (4-nitroacetophenone); 42VZT0U6YR (Heme); 76-22-2 (Camphor); EC 1.14.15.1 (Camphor 5-Monooxygenase)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180208
[Lr] Data última revisão:
180208
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170506
[St] Status:MEDLINE


  3 / 429 MEDLINE  
              first record previous record next record last record
seleciona
para imprimir
Fotocópia
Texto completo
[PMID]:28741929
[Au] Autor:Liou SH; Myers WK; Oswald JD; Britt RD; Goodin DB
[Ad] Endereço:Department of Chemistry, University of California , Davis, California 95616, United States.
[Ti] Título:Putidaredoxin Binds to the Same Site on Cytochrome P450cam in the Open and Closed Conformation.
[So] Source:Biochemistry;56(33):4371-4378, 2017 08 22.
[Is] ISSN:1520-4995
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Cytochrome P450 CYP101A1 (P450cam) hydroxylates camphor by receiving two distinct electrons from its unique reductase, putidaredoxin (Pdx). Upon binding ferric P450cam, Pdx is now known to trigger a conformational change in the enzyme. This Pdx-induced conversion may provide the trigger to coordinate enzyme turnover and protect the enzyme from oxidative damage, so the interactions responsible for this conversion are of significant interest at present. This proposed role for Pdx requires that its interactions with P450cam be different for the open and closed conformations. In this study, we show that the binding thermodynamics of Pdx does indeed differ in the predicted way when the conformation of P450cam is held in different states. However, double electron-electron resonance measurements of intermolecular distances in the Pdx/P450cam complex show that the geometry of the complex is nearly identical for the open and closed states of P450cam. These studies show that Pdx appears to make a single distinct interaction with its binding site on the enzyme and triggers the conformational change through very subtle structural interactions.
[Mh] Termos MeSH primário: Cânfora 5-Mono-Oxigenase/química
Ferredoxinas/química
Complexos Multiproteicos/química
Pseudomonas putida/química
[Mh] Termos MeSH secundário: Cânfora 5-Mono-Oxigenase/genética
Ferredoxinas/genética
Complexos Multiproteicos/genética
Estrutura Quaternária de Proteína
Pseudomonas putida/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Nm] Nome de substância:
0 (Ferredoxins); 0 (Multiprotein Complexes); 57087-75-9 (putidaredoxin); EC 1.14.15.1 (Camphor 5-Monooxygenase)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:171206
[Lr] Data última revisão:
171206
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170726
[St] Status:MEDLINE
[do] DOI:10.1021/acs.biochem.7b00564


  4 / 429 MEDLINE  
              first record previous record next record last record
seleciona
para imprimir
Fotocópia
Texto completo
[PMID]:28772002
[Au] Autor:Roth S; Funk I; Hofer M; Sieber V
[Ad] Endereço:Technical University of Munich, Chair of Chemistry of Biogenic Resources, Schulgasse 16, 94315, Straubing, Germany.
[Ti] Título:Chemoenzymatic Synthesis of a Novel Borneol-Based Polyester.
[So] Source:ChemSusChem;10(18):3574-3580, 2017 Sep 22.
[Is] ISSN:1864-564X
[Cp] País de publicação:Germany
[La] Idioma:eng
[Ab] Resumo:Terpenes are a class of natural compounds that have recently moved into the focus as a bio-based resource for chemical production, owing to their abundance, their mostly cyclic structures, and the presence of olefin or single hydroxy groups. To apply this raw material in new industrial fields, a second hydroxy group is inserted into borneol by cytochrome P450cam (CYP101) enzymes in a whole-cell catalytic biotransformation with Pseudomonas putida KT2440. Next, a semi-continuous batch system was developed to produce 5-exo-hydroxyborneol with a final concentration of 0.54 g L . The bifunctional terpene was then used for the synthesis of a bio-based polyester by a solvent-free polycondensation reaction. The resulting polymer showed a glass transition temperature of around 70 °C and a molecular weight in the range of 2000-4000 g mol (M ). These results show that whole-cell catalytic biotransformation of terpenes could lead to bio-based, higher-functionalized monomers, which might be basic raw materials for different fields of application, such as biopolymers.
[Mh] Termos MeSH primário: Bornanos/química
Cânfora 5-Mono-Oxigenase/metabolismo
Poliésteres/química
Poliésteres/metabolismo
[Mh] Termos MeSH secundário: Biocatálise
Biotransformação
Engenharia Genética
Polimerização
Pseudomonas putida/citologia
Pseudomonas putida/enzimologia
Pseudomonas putida/genética
Pseudomonas putida/metabolismo
Temperatura Ambiente
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Bornanes); 0 (Polyesters); EC 1.14.15.1 (Camphor 5-Monooxygenase); L88RA8N5EG (isoborneol)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171017
[Lr] Data última revisão:
171017
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170804
[St] Status:MEDLINE
[do] DOI:10.1002/cssc.201701146


  5 / 429 MEDLINE  
              first record previous record next record last record
seleciona
para imprimir
Fotocópia
Texto completo
[PMID]:28581729
[Au] Autor:Basom EJ; Manifold BA; Thielges MC
[Ad] Endereço:Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States.
[Ti] Título:Conformational Heterogeneity and the Affinity of Substrate Molecular Recognition by Cytochrome P450cam.
[So] Source:Biochemistry;56(25):3248-3256, 2017 Jun 27.
[Is] ISSN:1520-4995
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The broad and variable substrate specificity of cytochrome P450 enzymes makes them a model system for studying the determinants of protein molecular recognition. The archetypal cytochrome P450cam (P450cam) is a relatively specific P450, a feature once attributed to the high rigidity of its active site. However, increasingly studies have provided evidence of the importance of conformational changes to P450cam activity. Here we used infrared (IR) spectroscopy to investigate the molecular recognition of P450cam. Toward this goal, and to assess the influence of a hydrogen bond (H-bond) between active site residue Y96 and substrates, two variants in which Y96 is replaced by a cyanophenyl (Y96CNF) or phenyl (Y96F) group were characterized in complexes with the substrates camphor, isoborneol, and camphane. These combinations allow for a comparison of complexes in which the moieties on both the protein and substrate can serve as a H-bond donor, acceptor, or neither. The IR spectra of heme-bound CO and the site-specifically incorporated CN of Y96CNF were analyzed to characterize the number and nature of environments in each protein, both in the free and bound states. Although the IR spectra do not support the idea that protein-substrate H-bonding is central to P450cam recognition, the data altogether suggest that the differing conformational heterogeneity in the active site of the P450cam variants and changes in heterogeneity upon binding of different substrates likely contribute to their variable affinities via a conformational selection mechanism. This study further extends our understanding of the molecular recognition of archetypal P450cam and demonstrates the application of IR spectroscopy combined with selective protein modification to delineate protein-ligand interactions.
[Mh] Termos MeSH primário: Cânfora 5-Mono-Oxigenase/química
Cânfora 5-Mono-Oxigenase/metabolismo
Conformação Proteica
[Mh] Termos MeSH secundário: Cânfora 5-Mono-Oxigenase/genética
Domínio Catalítico
Cristalografia por Raios X
Seres Humanos
Ligações de Hidrogênio
Modelos Moleculares
Mutação/genética
Ligação Proteica
Especificidade por Substrato
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE
[Nm] Nome de substância:
EC 1.14.15.1 (Camphor 5-Monooxygenase)
[Em] Mês de entrada:1707
[Cu] Atualização por classe:170720
[Lr] Data última revisão:
170720
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170606
[St] Status:MEDLINE
[do] DOI:10.1021/acs.biochem.7b00238


  6 / 429 MEDLINE  
              first record previous record next record last record
seleciona
para imprimir
Fotocópia
[PMID]:27808504
[Au] Autor:Batabyal D; Lewis-Ballester A; Yeh SR; Poulos TL
[Ad] Endereço:Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California , Irvine, California 92697, United States.
[Ti] Título:A Comparative Analysis of the Effector Role of Redox Partner Binding in Bacterial P450s.
[So] Source:Biochemistry;55(47):6517-6523, 2016 Nov 29.
[Is] ISSN:1520-4995
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The camphor monooxygenase, cytochrome P450cam, exhibits a strict requirement for its own redox partner, putidaredoxin (Pdx), a two-iron-sulfur ferredoxin. The closest homologue to P450cam, CYP101D1, is structurally very similar, uses a similar redox partner, and exhibits nearly identical enzymatic properties in the monooxygenation of camphor to give the same single 5-exo-hydroxy camphor product. However, CYP101D1 does not strictly require its own ferredoxin (Arx) for activity because Pdx can support CYP101D1 catalysis but Arx cannot support P450cam catalysis. We have further examined the differences between these two P450s by determining the effect of spin equilibrium, redox properties, and stability of oxygen complexes. We find that Arx shifts the spin state equilibrium toward high-spin, which is the opposite of the effect of Pdx on P450cam. In both P450s, redox partner binding destabilizes the oxy-P450 complex but this effect is much weaker with CYP101D1. In addition, resonance Raman data show that structural perturbations observed in P450cam upon addition of Pdx are absent in CYP101D1. These data indicate that Arx does not play the same effector role in catalysis as Pdx does with P450cam. The most relevant structural difference between these two P450s centers on a catalytically important Asp residue required for proton-coupled electron transfer. We postulate that with P450cam larger Pdx-assisted motions are required to free this Asp for catalysis while the smaller number of restrictions in CYP101D1 precludes the need for redox partner-assisted structural changes.
[Mh] Termos MeSH primário: Proteínas de Bactérias/metabolismo
Cânfora 5-Mono-Oxigenase/metabolismo
Cânfora/metabolismo
Domínios Proteicos
[Mh] Termos MeSH secundário: Proteínas de Bactérias/química
Cânfora/química
Cânfora 5-Mono-Oxigenase/química
Domínio Catalítico
Cristalografia por Raios X
Transporte de Elétrons
Ferredoxinas/química
Ferredoxinas/metabolismo
Cinética
Modelos Moleculares
Oxirredução
Ligação Proteica
Espectrofotometria
Análise Espectral Raman
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Bacterial Proteins); 0 (Ferredoxins); 57087-75-9 (putidaredoxin); 76-22-2 (Camphor); EC 1.14.15.1 (Camphor 5-Monooxygenase)
[Em] Mês de entrada:1705
[Cu] Atualização por classe:170601
[Lr] Data última revisão:
170601
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161104
[St] Status:MEDLINE


  7 / 429 MEDLINE  
              first record previous record next record last record
seleciona
para imprimir
Fotocópia
[PMID]:27590809
[Au] Autor:Unterweger B; Bulach DM; Scoble J; Midgley DJ; Greenfield P; Lyras D; Johanesen P; Dumsday GJ
[Ad] Endereço:Department of Microbiology, Monash University, Clayton, VIC, Australia Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia CSIRO Manufacturing, Clayton, VIC, Australia.
[Ti] Título:CYP101J2, CYP101J3, and CYP101J4, 1,8-Cineole-Hydroxylating Cytochrome P450 Monooxygenases from Sphingobium yanoikuyae Strain B2.
[So] Source:Appl Environ Microbiol;82(22):6507-6517, 2016 Nov 15.
[Is] ISSN:1098-5336
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:We report the isolation and characterization of three new cytochrome P450 monooxygenases: CYP101J2, CYP101J3, and CYP101J4. These P450s were derived from Sphingobium yanoikuyae B2, a strain that was isolated from activated sludge based on its ability to fully mineralize 1,8-cineole. Genome sequencing of this strain in combination with purification of native 1,8-cineole-binding proteins enabled identification of 1,8-cineole-binding P450s. The P450 enzymes were cloned, heterologously expressed (N-terminally His tagged) in Escherichia coli BL21(DE3), purified, and spectroscopically characterized. Recombinant whole-cell biotransformation in E. coli demonstrated that all three P450s hydroxylate 1,8-cineole using electron transport partners from E. coli to yield a product putatively identified as (1S)-2α-hydroxy-1,8-cineole or (1R)-6α-hydroxy-1,8-cineole. The new P450s belong to the CYP101 family and share 47% and 44% identity with other 1,8-cineole-hydroxylating members found in Novosphingobium aromaticivorans and Pseudomonas putida Compared to P450 (CYP176A1), a 1,8-cineole-hydroxylating P450 from Citrobacter braakii, these enzymes share less than 30% amino acid sequence identity and hydroxylate 1,8-cineole in a different orientation. Expansion of the enzyme toolbox for modification of 1,8-cineole creates a starting point for use of hydroxylated derivatives in a range of industrial applications. IMPORTANCE: CYP101J2, CYP101J3, and CYP101J4 are cytochrome P450 monooxygenases from S. yanoikuyae B2 that hydroxylate the monoterpenoid 1,8-cineole. These enzymes not only play an important role in microbial degradation of this plant-based chemical but also provide an interesting route to synthesize oxygenated 1,8-cineole derivatives for applications as natural flavor and fragrance precursors or incorporation into polymers. The P450 cytochromes also provide an interesting basis from which to compare other enzymes with a similar function and expand the CYP101 family. This could eventually provide enough bacterial parental enzymes with similar amino acid sequences to enable in vitro evolution via DNA shuffling.
[Mh] Termos MeSH primário: Cânfora 5-Mono-Oxigenase/isolamento & purificação
Cânfora 5-Mono-Oxigenase/metabolismo
Cicloexanóis/metabolismo
Monoterpenos/metabolismo
Esgotos/microbiologia
Sphingomonadaceae/enzimologia
[Mh] Termos MeSH secundário: Biotransformação
Cânfora 5-Mono-Oxigenase/classificação
Cânfora 5-Mono-Oxigenase/genética
Citrobacter/enzimologia
Citrobacter/genética
Transporte de Elétrons
Escherichia coli/genética
Genoma Bacteriano
Hidroxilação
Microbiologia Industrial
Ligação Proteica
Pseudomonas putida/enzimologia
Pseudomonas putida/genética
Proteínas Recombinantes/metabolismo
Sphingomonadaceae/genética
Sphingomonadaceae/isolamento & purificação
Sphingomonadaceae/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Cyclohexanols); 0 (Monoterpenes); 0 (Recombinant Proteins); 0 (Sewage); EC 1.14.15.1 (Camphor 5-Monooxygenase); RV6J6604TK (eucalyptol)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171031
[Lr] Data última revisão:
171031
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160904
[St] Status:MEDLINE


  8 / 429 MEDLINE  
              first record previous record next record last record
seleciona
para imprimir
Fotocópia
Texto completo
[PMID]:26989997
[Au] Autor:Rydzewski J; Nowak W
[Ad] Endereço:Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University , Grudziadzka 5, 87-100 Torun, Poland.
[Ti] Título:Machine Learning Based Dimensionality Reduction Facilitates Ligand Diffusion Paths Assessment: A Case of Cytochrome P450cam.
[So] Source:J Chem Theory Comput;12(4):2110-20, 2016 Apr 12.
[Is] ISSN:1549-9626
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:In this work we propose an application of a nonlinear dimensionality reduction method to represent the high-dimensional configuration space of the ligand-protein dissociation process in a manner facilitating interpretation. Rugged ligand expulsion paths are mapped into 2-dimensional space. The mapping retains the main structural changes occurring during the dissociation. The topological similarity of the reduced paths may be easily studied using the Fréchet distances, and we show that this measure facilitates machine learning classification of the diffusion pathways. Further, low-dimensional configuration space allows for identification of residues active in transport during the ligand diffusion from a protein. The utility of this approach is illustrated by examination of the configuration space of cytochrome P450cam involved in expulsing camphor by means of enhanced all-atom molecular dynamics simulations. The expulsion trajectories are sampled and constructed on-the-fly during molecular dynamics simulations using the recently developed memetic algorithms [ Rydzewski, J.; Nowak, W. J. Chem. Phys. 2015 , 143 ( 12 ), 124101 ]. We show that the memetic algorithms are effective for enforcing the ligand diffusion and cavity exploration in the P450cam-camphor complex. Furthermore, we demonstrate that machine learning techniques are helpful in inspecting ligand diffusion landscapes and provide useful tools to examine structural changes accompanying rare events.
[Mh] Termos MeSH primário: Cânfora 5-Mono-Oxigenase/metabolismo
Cânfora/metabolismo
Pseudomonas putida/enzimologia
[Mh] Termos MeSH secundário: Cânfora/química
Cânfora 5-Mono-Oxigenase/química
Difusão
Ligantes
Aprendizado de Máquina
Simulação de Acoplamento Molecular
Simulação de Dinâmica Molecular
Conformação Proteica
Infecções por Pseudomonas/microbiologia
Pseudomonas putida/química
Pseudomonas putida/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Ligands); 76-22-2 (Camphor); EC 1.14.15.1 (Camphor 5-Monooxygenase)
[Em] Mês de entrada:1702
[Cu] Atualização por classe:170208
[Lr] Data última revisão:
170208
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160319
[St] Status:MEDLINE
[do] DOI:10.1021/acs.jctc.6b00212


  9 / 429 MEDLINE  
              first record previous record next record last record
seleciona
para imprimir
Fotocópia
PubMed Central Texto completo
Texto completo
[PMID]:26911901
[Au] Autor:Colthart AM; Tietz DR; Ni Y; Friedman JL; Dang M; Pochapsky TC
[Ad] Endereço:Departments of Chemistry and Biochemistry Brandeis University, 415 South St., Waltham MA 02454-9110, USA.
[Ti] Título:Detection of substrate-dependent conformational changes in the P450 fold by nuclear magnetic resonance.
[So] Source:Sci Rep;6:22035, 2016 Feb 25.
[Is] ISSN:2045-2322
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Cytochrome P450 monooxygenases typically catalyze the insertion of one atom of oxygen from O2 into unactivated carbon-hydrogen and carbon-carbon bonds, with concomitant reduction of the other oxygen atom to H2O by NAD(P)H. Comparison of the average structures of the camphor hydroxylase cytochrome P450(cam) (CYP101) obtained from residual dipolar coupling (RDC)-restrained molecular dynamics (MD) in the presence and absence of substrate camphor shows structural displacements resulting from the essential collapse of the active site upon substrate removal. This collapse has conformational consequences that extend across the protein structure, none of which were observed in analogous crystallographic structures. Mutations were made to test the involvement of the observed conformational changes in substrate binding and recognition. All of the mutations performed based upon the NMR-detected perturbations, even those remote from the active site, resulted in modified substrate selectivity, enzyme efficiency and/or haem iron spin state. The results demonstrate that solution NMR can provide insights into enzyme structure-function relationships that are difficult to obtain by other methods.
[Mh] Termos MeSH primário: Sistema Enzimático do Citocromo P-450/química
Modelos Moleculares
Ressonância Magnética Nuclear Biomolecular
Conformação Proteica
[Mh] Termos MeSH secundário: Sítios de Ligação
Cânfora 5-Mono-Oxigenase/química
Cânfora 5-Mono-Oxigenase/genética
Cânfora 5-Mono-Oxigenase/metabolismo
Domínio Catalítico
Sistema Enzimático do Citocromo P-450/genética
Sistema Enzimático do Citocromo P-450/metabolismo
Mutação
Ligação Proteica
Relação Estrutura-Atividade
Especificidade por Substrato
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
9035-51-2 (Cytochrome P-450 Enzyme System); EC 1.14.15.1 (Camphor 5-Monooxygenase)
[Em] Mês de entrada:1612
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160226
[St] Status:MEDLINE
[do] DOI:10.1038/srep22035


  10 / 429 MEDLINE  
              first record previous record
seleciona
para imprimir
Fotocópia
Texto completo
[PMID]:26460790
[Au] Autor:Vandemeulebroucke A; Aldag C; Stiebritz MT; Reiher M; Hilvert D
[Ad] Endereço:Laboratory of Organic Chemistry and ‡Laboratory of Physical Chemistry, ETH Zurich , CH-8093 Zurich, Switzerland.
[Ti] Título:Kinetic consequences of introducing a proximal selenocysteine ligand into cytochrome P450cam.
[So] Source:Biochemistry;54(44):6692-703, 2015 Nov 10.
[Is] ISSN:1520-4995
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The structural, electronic, and catalytic properties of cytochrome P450cam are subtly altered when the cysteine that coordinates to the heme iron is replaced with a selenocysteine. To map the effects of the sulfur-to-selenium substitution on the individual steps of the catalytic cycle, we conducted a comparative kinetic analysis of the selenoenzyme and its cysteine counterpart. Our results show that the more electron-donating selenolate ligand has only negligible effects on substrate, product, and oxygen binding, electron transfer, catalytic turnover, and coupling efficiency. Off-pathway reduction of oxygen to give superoxide is the only step significantly affected by the mutation. Incorporation of selenium accelerates this uncoupling reaction approximately 50-fold compared to sulfur, but because the second electron transfer step is much faster, the impact on overall catalytic turnover is minimal. Density functional theory calculations with pure and hybrid functionals suggest that superoxide formation is governed by a delicate interplay of spin distribution, spin state, and structural effects. In light of the remarkably similar electronic structures and energies calculated for the sulfur- and selenium-containing enzymes, the ability of the heavier atom to enhance the rate of spin crossover may account for the experimental observations. Because the selenoenzyme closely mimics wild-type P450cam, even at the level of individual steps in the reaction cycle, selenium represents a unique mechanistic probe for analyzing the role of the proximal ligand and spin crossovers in P450 chemistry.
[Mh] Termos MeSH primário: Cânfora 5-Mono-Oxigenase/metabolismo
Engenharia de Proteínas
Pseudomonas putida/enzimologia
Selenocisteína/metabolismo
[Mh] Termos MeSH secundário: Cânfora 5-Mono-Oxigenase/química
Cânfora 5-Mono-Oxigenase/genética
Cinética
Ligantes
Modelos Moleculares
Mutação
Oxirredução
Oxigênio/metabolismo
Pseudomonas putida/química
Pseudomonas putida/genética
Selenocisteína/química
Selenocisteína/genética
Superóxidos/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Ligands); 0CH9049VIS (Selenocysteine); 11062-77-4 (Superoxides); EC 1.14.15.1 (Camphor 5-Monooxygenase); S88TT14065 (Oxygen)
[Em] Mês de entrada:1602
[Cu] Atualização por classe:151110
[Lr] Data última revisão:
151110
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:151014
[St] Status:MEDLINE
[do] DOI:10.1021/acs.biochem.5b00939



página 1 de 43 ir para página                         
   


Refinar a pesquisa
  Base de dados : MEDLINE Formulário avançado   

    Pesquisar no campo  
1  
2
3
 
           



Search engine: iAH v2.6 powered by WWWISIS

BIREME/OPAS/OMS - Centro Latino-Americano e do Caribe de Informação em Ciências da Saúde